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Single molecule fluorescence spectroscopy of pH sensitive oligonucleotide switches
Branko Kolaric1, Michel Sliwa, Marco Brucale
1Katholieke Universiteit Leuven, Department Chemistry and Institute for Nanoscale Physics and Chemistry (INPAC), Celestijnenlaan 200F, Heverlee, B-3001, Belgium.
Oligonucleotide constructs act as pH-sensitive switches, opening and closing based on acidity. Single molecule studies reveal complete switching, unlike bulk observations, suggesting DNA construct association at higher concentrations.
Area of Science:
- Biochemistry
- Nanotechnology
- Molecular Biology
Background:
- Oligonucleotide constructs can function as pH-sensitive molecular switches.
- Fluorescence dye-quencher systems are used to monitor conformational changes.
Purpose of the Study:
- To investigate the pH-sensitive switching behavior of a duplex-triplex oligonucleotide construct.
- To compare bulk and single-molecule fluorescence observations of the switch.
Main Methods:
- Development of fluorescence dye-quencher substituted oligonucleotide constructs.
- Bulk fluorescence spectroscopy.
- Single-molecule fluorescence spectroscopy.
Main Results:
- Bulk measurements showed partial fluorescence quenching, attributed to intermolecular interactions.
- Single-molecule measurements demonstrated complete switching of individual DNA constructs.
- Observed behavior suggests DNA construct association at higher concentrations.
Conclusions:
- Individual oligonucleotide constructs exhibit complete pH-sensitive switching.
- Intermolecular interactions in bulk measurements can obscure the full switching capability.
- Concentration-dependent association influences the observed behavior of DNA nanostructures.
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